ZhaoImmuneLiverData: Obtain the Zhao immune liver data

Description Usage Arguments Details Value Author(s) References Examples

View source: R/ZhaoImmuneLiverData.R

Description

Obtain the human liver immune single-cell RNA-seq data from Zhao et al. (2020).

Usage

1

Arguments

location

Logical scalar indicating whether genomic coordinates should be returned.

filter

Logical scalar indicating if the filtered subset should be returned.

Details

Column metadata contains various cell labels as provided by the authors. Some of these labels required assembly on our part:

We guessed the sample for each cell by assuming that the GEM group numbers match the order of samples in GSE125188. We also assumed that “donor 4” is a typo, given that the paper only mentions 3 donors.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output. Note that this is only performed if ensembl=TRUE.

If filter=TRUE, only cells that have been used in the original analysis are returned. Otherwise, the cells used are specified in the retained column of the colData.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/zhao-immune-liver.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Zhao J et al. (2020). Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discov 6, 22.

Examples

1
sce.zhao <- ZhaoImmuneLiverData()

drisso/scRNAseq documentation built on Feb. 16, 2021, 1:18 a.m.